Each nucleotide monomer consists of a __, __ and a __. The _ of one nucleotide is attached to the sugar of the next, resulting in a __ of alternating phosphates and sugars from which the bases project. The __ strand has directionality, fromt eh 5' end (with the __) to the 3' end (with the __). 5' and 3' refer to the numbers assigned to the carbons in the sugar ring.

nitrogenous base (A,C,T, or G)

phosphate group

deoxyribose

phosphate

"backbone"

polynucleotide

phosphate group

-OH group

The DNA double helix is __, curving up to the right. The two strands are held together by __ between the nitrogenous bases, which are paired in the interior of the double helix.

right-handed

H bonds

Strong __ link the units of each strand, while weaker __ hold one strand to the other. The strands are __, meaning that they are oriented in opposite directions.

covalent bonds

hydrogen bonds

antiparallel

__ between the stacked pairs play a major role in holding the DNA molecule together.

Van der Waals interactions

The pairing of a purine + purine are __

too wide

The pairing of a pyrimidine and a pyrimidine are __

too narrow

The parent molecule has two __ strands of DNA. Each base is paired by __ with its specific partner, A with T, and G with C.

complementary

hydrogen bonds

Model stating that the two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.

conservative model

Model stating that the two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand.

semiconservative model

Model stating that each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

dispersive model

In the circular chromosome of E. coli and many other bacteria, only __ origin of replication is present.

one

__ unwinds and separates the parental DNA strands.

helicase

__ stabilize the unwound parental strands.

Single-strand binding proteins

__ breaks, swivels and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding.

topoisomerase

__ synthesizes RNA primers, using the parental DNA as a template.

primase

__ catalyzes the addition of a nucleoside triphosphate to the 3' end of a growing DNA strand, with the release of two phosphates.

DNA pol

__ shaped like a cupped hand, is closely associated with a protein called the __ that encircles the newly synthesized double helix like a doughnut. The sliding clamp moves DNA pol III along teh DNA template strand.

DNA pol III

sliding clamp

1) __ joins RNA nucleotides in to a primer.
2) __ adds DNA nucleotides to the primer, forming __ 1.
3) After reaching teh next RNA primer to the right, __ detaches.
4) After fragment 2 is primed __ adds DNA nucleotides until it reaches the fragment 1 primer and detaches.
5) __ replaces the RNA with DNA, adding to the 3' end of fragment 2.
6) __ forms a bond between the newest DNA and the DNA of fragment 1.
7) The __ in this region is now complete.

Primase

DNA pol III

Okasazi fragment

DNA pol III x2

DNA pol I

DNA ligase

lagging strand

1) __ unwinds the parental double helix.

helicase

2) Molecules of __ stabilize the unwound template strands.

single-strand binding protein

3) The leading strand is synthesized continuously in the 5'--> 3' direction by __.

DNA pol III

4) __ begins synthesis of the RNA primer for the fifth __.

primase

okaszi fragment

5) __ is completing synthesis of the fourth fragment. WHen it reaches the RNA priner on the third fragment, it will dissociate, move to the __, and add DNA nucleotides to the 3' end of the fifth fragment primer.

DNA pol III

replication fork

3) __ removes the primer from the 5' end of the second fragment, replacing it with DNA nucleotides that it adds one by one to the 3' end of the third fragment. The replacement of the last RNA nucleotide with DNA leaves the sugar phosphate backbone with a free 3' end.

DNA pol I

7) __ bonds the 3' end of the second fragment to the 5' end of the first fragment.

DNA ligase

unwinds parental double helix at the replcation forks

helicase

binds to and stabilizes single-straded DNA until it can be used as a template

synthesizes an RNA primer at 5' end of leading strand and of each Okazaki fragment of lagging strand

primase

Using parental DNA as a template, synthesizes new DNA strand by covalently adding nucleotides to the 3' end of a pre-existing DNA strand or RNA primer

DNA pol III

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

DNA pol I

Joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand

DNA ligase

Chromatin Packing in a Eukaryotic Chromosome
Name the 6 levels.

DNA, the double helix

Histones

Nucleosomes, or "beads on a string" (10 nm fiber)

30 nm fiber

Looped Domains (300 nm fiber)

Metaphse chromosome

Proteins called __ are responsible for hte first level of DNA packing in chromatin. Athough each __ is small- containing about 100 amino acids- the total mass of __ in chromatin approximately equals the mass of DNA. More than a fifth of a __ amino acids are positively charged (lysine or arginine) and bind tightly to the negatively charged DNA.

histones x3

Four types of histones are most common in chromatin: __, __, __ and __. The histones are very similar among eukaryotes. The apparent conservation of __genes during evolution probably reflects the pivotal role of __ in organizing DNA within cells. The four main types of histones are critical to the next level of DNA packing. (A fifth type of histone, called __, is involved in a further stage of packing.)

H2A

H2B

H3

H4

histone x2

H1

In EM, unfolded chromatin is __ in diameter. SUch chromatin resembles beads on a string. Each bead is a __, the basic unit of DNA packing; the string between beads is called __.

a nucleosone

linker DNA

A __ consists of DNA wound twice around a protein core composed of two molecules each of the four main __ types. The amino end (N-terminus) of each histone (__) extends outward from the __.

nucleosome

histone

histone tail

nucleosome

In the __, the __ leave the DNA only briefly during DNA replication. Generally, they do the same during gene expression, another process that requires access to DNA by the cell's molecular machinery.

cell cycle

histones

The next level of packing (4) is due to interactions between the _- of one _- and teh __ and __ on either side. A fiftth histone, __, is involved at this level. These interactions cause the extended 10 nm fiber to coil or fold, forming a chromatin fiber roughly 30 nm in thickness, the __. Although the 30-nm fiber is quite prevalent in the interphase nucleus the packing arrangemnent of __ in this form of chromatin is still a matter of some debate.

histone tails

nucleosome

linker DNA

nucleosomes

H1

30 nm fiber

nucleosomes

The 30 nm fiber in turn forms loops called __ attached to a chromosome __ made of proteins, thus making upa __. The __ is rich in one type of __, and H1 molecules also appear to be present.

looped domains

scaffold

300 nm fiber

scaffold

topoisomerase

In a mitotic chromosome, the _ themselves ccoil and fold in a manner not yet fully understood, further compacting all the chromatin to produce the characteristic metaphase chromosome. The width of one chromatid is __. Particular genes always end up located at the same places in metaphase chromosomes, indicating that the packing steps are highly specific and precise.